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cljam.io.bcf.writer


write-variantsclj

(write-variants w variants)

Writes data lines on writer. Returns nil. variants must be a sequence of parsed or VCF-style maps. e.g.

(write-variants [{:chr "19", :pos 111, :id nil, :ref "A", :alt ["C"], :qual 9.6, :filter [:PASS], :info {:DP 4}, :FORMAT [:GT :HQ] ...} ...])

Writes data lines on writer. Returns nil. `variants` must be a sequence of
parsed or VCF-style maps.
e.g.

  (write-variants [{:chr "19", :pos 111, :id nil, :ref "A",
                    :alt ["C"], :qual 9.6, :filter [:PASS], :info {:DP 4},
                    :FORMAT [:GT :HQ] ...} ...])
sourceraw docstring

writerclj

(writer f meta-info header)

Returns an open cljam.bcf.BCFWriter of f. Meta-information lines and a header line will be written in this function. Should be used inside with-open to ensure the Writer is properly closed. e.g.

(with-open [wtr (writer "out.bcf" {:file-date "20090805", :source "myImpu..." ...} ["CHROM" "POS" "ID" "REF" "ALT" ...])] (WRITING-BCF))

Returns an open cljam.bcf.BCFWriter of f.
Meta-information lines and a header line will be written in this function.
Should be used inside with-open to ensure the Writer is properly closed. e.g.

  (with-open [wtr (writer "out.bcf"
                          {:file-date "20090805", :source "myImpu..." ...}
                          ["CHROM" "POS" "ID" "REF" "ALT" ...])]
    (WRITING-BCF))
sourceraw docstring

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